rs371047262
Variant names:
Your query was ambiguous. Multiple possible variants found:
- chr17-31232043-ATTTTTTTTTTTTTTT-A
- chr17-31232043-ATTTTTTTTTTTTTTT-AT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_001042492.3(NF1):c.3198-18_3198-4delTTTTTTTTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000022 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000036 ( 1 hom. )
Failed GnomAD Quality Control
Consequence
NF1
NM_001042492.3 splice_region, intron
NM_001042492.3 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.14
Genes affected
NF1 (HGNC:7765): (neurofibromin 1) This gene product appears to function as a negative regulator of the ras signal transduction pathway. Mutations in this gene have been linked to neurofibromatosis type 1, juvenile myelomonocytic leukemia and Watson syndrome. The mRNA for this gene is subject to RNA editing (CGA>UGA->Arg1306Term) resulting in premature translation termination. Alternatively spliced transcript variants encoding different isoforms have also been described for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| NF1 | NM_001042492.3 | c.3198-18_3198-4delTTTTTTTTTTTTTTT | splice_region_variant, intron_variant | Intron 24 of 57 | ENST00000358273.9 | NP_001035957.1 | ||
| NF1 | NM_000267.3 | c.3198-18_3198-4delTTTTTTTTTTTTTTT | splice_region_variant, intron_variant | Intron 24 of 56 | NP_000258.1 |
Ensembl
Frequencies
GnomAD3 genomes 0.0000220 AC: 2AN: 90908Hom.: 0 Cov.: 0
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000361 AC: 18AN: 499014Hom.: 1 AF XY: 0.0000419 AC XY: 11AN XY: 262428
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GnomAD4 genome 0.0000220 AC: 2AN: 90908Hom.: 0 Cov.: 0 AF XY: 0.0000238 AC XY: 1AN XY: 42040
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hereditary cancer-predisposing syndrome;CN230736:Cardiovascular phenotype Benign:1
Dec 16, 2024
Ambry Genetics
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at